--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Nov 03 17:22:08 WET 2017 codeml.models=0 1 2 3 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=CLUSTALW2 tcoffee.params= tcoffee.maxSeqs=0 codeml.bin=codeml mrbayes.tburnin=2500 codeml.dir= input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb_adops tcoffee.bin=t_coffee_ADOPS mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta= input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Use the harmonic mean for Bayes factor comparisons of models) (Values are saved to the file /opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -8620.95 -8642.28 2 -8622.46 -8640.30 -------------------------------------- TOTAL -8621.44 -8641.71 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": Summaries are based on a total of 3002 samples from 2 runs. Each run produced 2001 samples of which 1501 samples were included. Parameter summaries saved to file "/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.662669 0.003710 1.545015 1.779488 1.661510 1458.38 1479.69 1.000 r(A<->C){all} 0.117137 0.000123 0.094345 0.138212 0.116956 833.18 871.08 1.000 r(A<->G){all} 0.303239 0.000295 0.269569 0.335507 0.303244 650.14 680.13 1.000 r(A<->T){all} 0.077738 0.000048 0.065472 0.092078 0.077442 860.53 1017.00 1.002 r(C<->G){all} 0.153593 0.000196 0.126320 0.180436 0.153288 900.49 911.31 1.000 r(C<->T){all} 0.263002 0.000250 0.232186 0.294656 0.262471 701.74 743.14 1.000 r(G<->T){all} 0.085291 0.000073 0.067937 0.101739 0.085081 974.89 1039.56 1.001 pi(A){all} 0.294570 0.000115 0.274350 0.316345 0.294519 853.71 978.11 1.000 pi(C){all} 0.170549 0.000070 0.155259 0.187312 0.170326 736.60 778.84 1.000 pi(G){all} 0.194103 0.000076 0.177129 0.211534 0.194013 775.94 805.79 1.000 pi(T){all} 0.340777 0.000128 0.319727 0.363873 0.340775 1021.92 1085.50 1.000 alpha{1,2} 0.973170 0.017761 0.719502 1.225681 0.955347 1269.56 1278.29 1.000 alpha{3} 2.116155 0.209839 1.365843 3.040421 2.044388 1207.72 1317.74 1.000 pinvar{all} 0.028050 0.000572 0.000001 0.074940 0.021913 1133.52 1212.89 1.000 ------------------------------------------------------------------------------------------------------ * Convergence diagnostic (ESS = Estimated Sample Size); min and avg values correspond to minimal and average ESS among runs. ESS value below 100 may indicate that the parameter is undersampled. + Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman and Rubin, 1992) should approach 1.0 as runs converge. Setting sumt conformat to Simple --- CODEML SUMMARY Model 1: NearlyNeutral -5546.008641 Model 2: PositiveSelection -5506.94212 Model 0: one-ratio -5690.898501 Model 3: discrete -5506.465714 Model 7: beta -5555.868136 Model 8: beta&w>1 -5510.055124 Model 0 vs 1 289.77971999999863 Model 2 vs 1 78.1330420000013 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S28_SFBB1) Pr(w>1) post mean +- SE for w 5 N 0.998** 3.919 11 R 0.998** 3.921 15 P 0.950 3.780 44 L 0.663 2.939 51 E 0.998** 3.920 64 A 0.910 3.663 75 G 0.653 2.909 99 I 0.998** 3.919 101 T 1.000** 3.926 162 E 0.721 3.111 165 C 0.996** 3.914 181 T 1.000** 3.926 183 E 0.925 3.706 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S28_SFBB1) Pr(w>1) post mean +- SE for w 5 N 0.997** 4.017 +- 0.576 11 R 0.998** 4.020 +- 0.569 15 P 0.929 3.795 +- 0.934 44 L 0.596 2.732 +- 1.478 51 E 0.998** 4.020 +- 0.570 64 A 0.876 3.623 +- 1.109 75 G 0.595 2.745 +- 1.495 99 I 0.997** 4.018 +- 0.574 101 T 1.000** 4.026 +- 0.553 162 E 0.644 2.863 +- 1.443 165 C 0.995** 4.012 +- 0.590 181 T 1.000** 4.027 +- 0.550 183 E 0.900 3.706 +- 1.039 Model 8 vs 7 91.62602399999923 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S28_SFBB1) Pr(w>1) post mean +- SE for w 5 N 0.999** 3.448 11 R 0.999** 3.449 15 P 0.979* 3.396 44 L 0.823 2.997 51 E 0.999** 3.448 53 G 0.537 2.255 64 A 0.962* 3.354 75 G 0.795 2.920 91 R 0.659 2.576 99 I 0.999** 3.448 101 T 1.000** 3.451 162 E 0.878 3.139 165 C 0.998** 3.446 181 T 1.000** 3.451 183 E 0.965* 3.362 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S28_SFBB1) Pr(w>1) post mean +- SE for w 5 N 0.999** 3.579 +- 0.320 11 R 0.999** 3.580 +- 0.317 15 P 0.967* 3.491 +- 0.563 44 L 0.745 2.875 +- 1.184 51 E 0.999** 3.579 +- 0.320 64 A 0.942 3.422 +- 0.689 75 G 0.722 2.813 +- 1.229 91 R 0.544 2.321 +- 1.323 99 I 0.998** 3.579 +- 0.321 101 T 1.000** 3.583 +- 0.306 162 E 0.807 3.041 +- 1.071 165 C 0.997** 3.576 +- 0.334 181 T 1.000** 3.583 +- 0.304 183 E 0.949 3.442 +- 0.661